The DOE Systems Biology Knowledgebase: Introduction to KBase for Plant Researchers

The U.S. Department of Energy Systems Biology Knowledgebase (KBase, http://kbase.us) provides a computational environment to meet the key challenges of systems biology: predicting and ultimately designing biological function. KBase is distinguished as a knowledgebase that supports the sharing and integration of biological data and any related analysis, modeling, and simulation, not simply a database or a workbench that serves data with canned analyses.

This introduction will briefly cover plant resources available in KBase. KBase does integrate commonly used core tools along with reference and experimental data, and overlays them with new capabilities for visualization, exploration, and predictive analysis designed to accelerate understanding of plants, microbes, and their communities. It provides open access to quality-controlled data and high-performance modeling and simulation tools that enable researchers to build new knowledge, interpret missing information necessary for predictive modeling, test hypotheses, design experiments, and share findings that can be reproduced and extended by others.

User-furnished data can be uploaded, analyzed using high-performance bioinformatics tools, and overlaid visually and analytically on KBase-provided data.

KBase online tutorials such as Build Plant Metabolic Model found at http://kbase.us/tutorials/ provide a good starting place to understand how KBase might be useful in your research and how to get started.